High-resolution image analysis of digitized pathology slides coupled with molecular data has enormous potential to provide additional information for stratifying patients in terms of prognosis and therapy. We propose to develop methods, analytic pipelines, and data management tools that will make it feasible to systematically carry out large-scale comparative analyses of brain tumor histological features and of patterns of protein and gene expression. We will develop information models to manage information associated with analysis of brain tumor whole virtual slide data. These models will capture information about context relating to patient data, specimen preparation, and special stains, human observations involving histological classification and characteristics, algorithmic composition, parameterization and input data corresponding to analysis pipelines, and algorithm and human-described segmentations, features, and classifications. We will implement middleware for high-performance database and query support for queries that selects subsets of image data and results based on metadata on images and provenance information; that compare features, spatial structures, and classifications obtained from multiple algorithms as well as human markups; and that compare statistical and summary information on features and classifications across multiple image datasets. Using the information models and middleware, we will carry out analysis studies needed to determine the relationship between image analysis derived tumor information and clinical outcome, gene expression category, genetic gains and losses, and methylation status. We will employ a novel automated multiplex quantum dot immunohistochemistry with peptide controls and quantitative image analysis methodology to map the activity of signal transduction pathways and transcriptional networks relative to the tumor microenvironment using histology feature descriptions. We will leverage multivariate data fusion techniques to simultaneously take into account potential correlations and relationships among the measured image features, molecular signatures to predict patient outcomes. We will deploy a data repository populated with images, features, analysis pipelines, provenance information, and analytic results from our project. This repository will provide a publicly available resource for brain tumor research. All software and information models developed in this project will be open source and free for research use.